rs688 Rat Genome Database

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Variant: rs688 -  Homo sapiens

RGD ID: 10055554
RS ID: rs688
ClinVar ID: CV198016
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: LDLR  
Reference Nucleotide: C
Variant Nucleotide: T
Position
Assembly Chr Position
GRCh37 19 11,227,602
GRCh38 19 11,116,926
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Prevalence Trait Synonyms
LRG_274t1:c.1773C>T
NC_000019.10:g.11116926C>T
NC_000019.9:g.11227602C>T
NP_000518.1:p.Asn591=
More... 		09/16/2020 synonymous variant benign|likely benign|conflicting interpretations of pathogenicity 1-9 / 1 000 000 AllHighlyPenetrant; Fredrickson type IIa hyperlipoproteinemia; Hyper-beta-lipoproteinemia; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; HYPERCHOLESTEROLEMIA, FAMILIAL, MODIFIER OF; HYPERCHOLESTEROLEMIC XANTHOMATOSIS, FAMILIAL; Hyperlipoproteinemia type 2; Hyperlipoproteinemia Type II; Hyperlipoproteinemia Type IIa; LDL RECEPTOR DISORDER; none provided
Disease Annotations     Click to see Annotation Detail View

GWAS Catalog Data
GWAS Catalog Study Disease Trait Study Size Risk Allele Risk Allele Frequency P Value P Value MLOG SNP Passing QC Reported Odds Ratio or Beta-coefficient Ontology Accession PubMed
GCST007141 Low density lipoprotein cholesterol levels 76,627 European ancestry individuals, 7,795 Hispanic individuals, 6,855 East Asian ancestry individuals, 2,958 African American individuals, 439 South Asian ancestry individuals C 0.578 5E-30 29.30102999566398 Affymetrix [at least 7091467] (imputed) 0.058 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:29507422
GCST007141 Low density lipoprotein cholesterol levels 76,627 European ancestry individuals, 7,795 Hispanic individuals, 6,855 East Asian ancestry individuals, 2,958 African American individuals, 439 South Asian ancestry individuals C NR 2E-32 31.69897000433602 Affymetrix [at least 7091467] (imputed) 0.057 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:29507422
GCST008676 LDL cholesterol levels up to 23,353 African ancestry individuals, 13,171 Asian ancestry individuals, up to 82,522 European ancestry individuals, 6,646 Hispanic individuals T 0.4002 5E-27 26.30102999566398 Affymetrix, Illumina, Perlegen [NR] (imputed) 1.747 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:30926973
GCST010060 Cholesterol 6,840 Korean ancestry individuals T 0.136 7E-8 7.154901959985743 Affymetrix [305158] 3.402 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:31902109
GCST008037 Low density lipoprotein cholesterol levels 9,720 African American individuals, 17,373 Hispanic/Latino individuals, 2,316 Asian ancestry individuals, 1,900 Native Hawaiian ancestry individuals, 591 Native American ancestry individuals, 321 individuals ? NR 1E-8 8.0 Illumina [31808917] (imputed) 2.007519 low density lipoprotein cholesterol measurement (EFO:0004611)
 PMID:31217584
GCST008045 Total cholesterol levels 10,137 African American individuals, 17,802 Hispanic/Latino individuals, 2,387 Asian ancestry individuals, 1,915 Native Hawaiian ancestry individuals, 604 Native American ancestry individuals, 340 individuals ? NR 2E-8 7.698970004336019 Illumina [32003504] (imputed) 2.235765 total cholesterol measurement (EFO:0004574)
 PMID:31217584
GCST007143 Total cholesterol levels 76,627 European ancestry individuals, 7,795 Hispanic individuals, 6,855 East Asian ancestry individuals, 2,958 African American individuals, 439 South Asian ancestry individuals C 0.578 1E-25 25.0 Affymetrix [at least 7091467] (imputed) 0.052 total cholesterol measurement (EFO:0004574)
 PMID:29507422
GCST007143 Total cholesterol levels 76,627 European ancestry individuals, 7,795 Hispanic individuals, 6,855 East Asian ancestry individuals, 2,958 African American individuals, 439 South Asian ancestry individuals C NR 4E-28 27.397940008672037 Affymetrix [at least 7091467] (imputed) 0.052 total cholesterol measurement (EFO:0004574)
 PMID:29507422

Variant Details
Variant Transcripts
Gene Symbol:LDLR
Accession:NM_001195803
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 464
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVN
RCIPQFWRCDGQVDCDNGSDEQGCPVATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSG
ECITLDKVCNMARDCRDWSDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQL
CVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLS
QRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPV
HGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAH
PFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQPREAEAAVATQETSTVRLKVSSTAVRT
QHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGNEKKPSSVRALSIVLPIVLLVFLCLGVFLLWKNWRLKNI
NSINFDNPVYQKTTEDEVHICHNQDGYSYPSRQMVSLEDDVA*

Gene Symbol:LDLR
Accession:NM_001195798
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 591
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVN
RCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTC
IPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDE
FQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLD
NNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAY
LFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLA
VDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENI
QWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVN
LLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA
TQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGNEKKPSSVRALSIVLPIVLLV
FLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICHNQDGYSYPSMVSLEDDVA*

Gene Symbol:LDLR
Accession:NM_001195800
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 423
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVN
RCIPQFWRCDGQVDCDNGSDEQGCLTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLDNNGGCSHV
CNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHE
VRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNI
YWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITL
DLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLS
PEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVATQETSTVR
LKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGNEKKPSSVRALSIVLPIVLLVFLCLGVFL
LWKNWRLKNINSINFDNPVYQKTTEDEVHICHNQDGYSYPSRQMVSLEDDVA*

Gene Symbol:LDLR
Accession:NM_000527
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 591
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVN
RCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTC
IPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDE
FQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLD
NNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAY
LFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLA
VDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENI
QWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVN
LLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA
TQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGNEKKPSSVRALSIVLPIVLLV
FLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICHNQDGYSYPSRQMVSLEDDVA*

Gene Symbol:LDLR
Accession:NM_001195799
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 550
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCSPKTCSQDEFRCHDGKC
ISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFE
FHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDEFQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNK
FKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDP
DTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRI
YWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRA
IVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILED
EKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLC
LPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVATQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTT
VEIVTMSHQALGDVAGRGNEKKPSSVRALSIVLPIVLLVFLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICHN
QDGYSYPSRQMVSLEDDVA*

Gene Symbol:LDLR
Accession:XM_011528010
Location:EXON
Amino Acid Prediction: N to N (synonymous)
Amino Acid Position: 591
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQETCLSVTCKSGDFSCGGRVN
RCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTC
IPQLWACDNDPDCEDGSDEWPQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDE
FQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDWSDEPIKECGTNECLD
NNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAY
LFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLA
VDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENI
QWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVN
LLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA
TQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQVLLVFLCLGVFLLWKNWRLKNINSINFDNP
VYQKTTEDEVHICHNQDGYSYPSRQMVSLEDDVA*

Gene Symbol:LDLR
Accession:NM_001406861
Location:INTRON

Gene Symbol:LDLR
Accession:XM_047438831
Location:INTRON

Variant Samples
Additional References at PubMed
PMID:11641914   PMID:12730724   PMID:24033266   PMID:25741868   PMID:28492532  


Additional Information

Database Acc Id Source(s)
ClinVar RCV000182338 CLINVAR
  RCV000237654 CLINVAR
  RCV001275781 CLINVAR
  RCV001812171 CLINVAR
  RCV002399653 CLINVAR
dbSNP (RS) rs688 CLINVAR
GWAS Catalog GCST008676 GWAS Catalog
  GCST010060 GWAS Catalog
MedGen C0020445 CLINVAR
  C0745103 CLINVAR
  C3661900 CLINVAR
  CN169374 CLINVAR
  CN230736 CLINVAR
NCBI Gene LDLR CLINVAR
OMIM 143890 CLINVAR
  144400 CLINVAR
  606945 CLINVAR
SNOMED CT 397915002 CLINVAR
  398036000 CLINVAR